Discovery of Mcl-1 inhibitors from integrated high throughput and virtual screening

Abstract

Protein-protein interactions (PPIs) represent important and promising therapeutic targets that are associated with the regulation of various molecular pathways, particularly in cancer. Although they were once considered “undruggable,” the recent advances in screening strategies, structure-based design, and elucidating the nature of hot spots on PPI interfaces, have led to the discovery and development of successful small-molecule inhibitors. In this report, we are describing an integrated high-throughput and computational screening approach to enable the discovery of small-molecule PPI inhibitors of the anti-apoptotic protein, Mcl-1. Applying this strategy, followed by biochemical, biophysical, and biological characterization, nineteen new chemical scaffolds were discovered and validated as Mcl-1 inhibitors. A novel series of Mcl-1 inhibitors was designed and synthesized based on the identified difuryl-triazine core scaffold and structure-activity studies were undertaken to improve the binding affinity to Mcl-1. Compounds with improved in vitro binding potency demonstrated on-target activity in cell-based studies. The obtained results demonstrate that structure-based analysis complements the experimental high-throughput screening in identifying novel PPI inhibitor scaffolds and guides follow-up medicinal chemistry efforts. Furthermore, our work provides an example that can be applied to the analysis of available screening data against numerous targets in the PubChem BioAssay Database, leading to the identification of promising lead compounds, fuelling drug discovery pipelines.

Drug Repurposing: Deferasirox Inhibits the Anti-Apoptotic Activity of Mcl-1

“…Moreover, the NMR data suggested an interaction with Gly219, Val220 and Val216, part of the P4 pocket, for both ligands. This observation was also highlighted from similar NMR data reported by Mady et al, 68 for a set of Mcl-1 inhibitors. These interactions at the P4 pocket might rise from a non-direct effect due to the presence of aromatic rings (ring-current effect) as we have previously discussed for Pyridoclax 36 for instance.…”

Rationally Designed Polypharmacology: α‐Helix Mimetics as Dual Inhibitors of the Oncoproteins Mcl‐1 and HDM2

“…[44][45][46] Importantly, there is a conserved arginine residue on pro-life proteins (Arg263 in Mcl-1) that forms a salt bridge with Asp67 on the Bim α-helix at the i + 5 position. [47] Additionally, there is an aspartate residue in an analogous location (i + 2) in p53TAD (Asp21), that helps maintain the integrity of the helix rather than engage in recognition. [48] We set out to capitalize on these similarities across both α-helices towards the discovery of dual inhibitors of Mcl-1 and HDM2.…”

Discovery and Characterization of 2,5-Substituted Benzoic Acid Dual Inhibitors of the Anti-apoptotic Mcl-1 and Bfl-1 Proteins

“…Aside from the on-target toxicity concerns, Bcl-xL remains an important therapeutic target, especially in solid tumors, therefore development of selective Bcl-xL inhibitors remains an attractive approach. , The selective Bcl-2 inhibitor, ABT-199 or venetoclax, is the first BH3 mimetic with granted FDA approval for its success in treating chronic lymphocytic leukemia and is currently being evaluated in numerous clinical trials for various indications. , The need for selective Mcl-1 inhibitors emerged from the observance of Mcl-1 as a prominent resistance factor to other BH3 mimetics, as well as to many targeted chemo- and radiotherapies . This need was addressed by selective Mcl-1 inhibitors developed by our group − and others, both in academia − and industry. − The work on selective Mcl-1 inhibitors has culminated to several compounds now being evaluated in phase I clinical trials for the treatment of hematologic malignancies as a single agent (ClinicalTrials.gov; NCT02675452, NCT03465540, NCT02979366, NCT02992483, NCT03218683) and in combination with venetoclax (ClinicalTrials.gov; NCT03672695). There is still a need, however, to effectively target Bfl-1 with drug-like molecules, as the main successes have come from selective peptides. − We and others, using biochemical screening assays, have identified hit small molecule inhibitors of Bfl-1 which require further optimization. , A recent study identified bicyclic stapled peptides as dual Mcl-1/Bfl-1 inhibitors with cellular activity and demonstrated an opportunity to develop Noxa-mimetic type inhibitors …”

“…This need was addressed by selective Mcl-1 inhibitors developed by our group − and others, both in academia − and industry. − The work on selective Mcl-1 inhibitors has culminated to several compounds now being evaluated in phase I clinical trials for the treatment of hematologic malignancies as a single agent (ClinicalTrials.gov; NCT02675452, NCT03465540, NCT02979366, NCT02992483, NCT03218683) and in combination with venetoclax (ClinicalTrials.gov; NCT03672695). There is still a need, however, to effectively target Bfl-1 with drug-like molecules, as the main successes have come from selective peptides. − We and others, using biochemical screening assays, have identified hit small molecule inhibitors of Bfl-1 which require further optimization. , A recent study identified bicyclic stapled peptides as dual Mcl-1/Bfl-1 inhibitors with cellular activity and demonstrated an opportunity to develop Noxa-mimetic type inhibitors …”

“…Our recent work utilizing an integrated high throughput and virtual screening approach yielded several scaffolds that showed binding to Mcl-1 and Bfl-1, including compound 19 (here referred to as 19SR ). , Our screening strategy using the Noxa pharmacophore to funnel high throughput hits likely selected for molecular scaffolds that display a dual Mcl-1/Bfl-1 binding profile . In this manuscript, we describe the further development of this hit molecule, 19SR , by redesigning the chemical core structure (Figure A).…”